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Calcium in PDB 5ele: Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y

Protein crystallography data

The structure of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y, PDB code: 5ele was solved by J.E.Heggelund, D.Burschowsky, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.543, 82.973, 196.555, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y (pdb code 5ele). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y, PDB code: 5ele:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5ele

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Calcium binding site 1 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:14.5
occ:1.00
 O6 A:BCN205 1.9 29.6 1.0
O4 A:BCN205 2.3 22.8 1.0
O22 A:BCN205 2.3 16.7 1.0
OE1 A:GLU79 2.4 16.2 1.0
OE2 F:GLU79 2.4 17.5 1.0
O A:HOH302 2.4 25.6 1.0
OE2 A:GLU79 2.6 16.3 1.0
CD A:GLU79 2.8 17.5 1.0
C6 A:BCN205 3.0 27.7 1.0
N1 A:BCN205 3.1 22.3 1.0
C2 A:BCN205 3.2 18.8 1.0
C4 A:BCN205 3.2 22.2 1.0
C3 A:BCN205 3.2 23.3 1.0
C1 A:BCN205 3.4 20.8 1.0
C5 A:BCN205 3.5 23.4 1.0
CD F:GLU79 3.5 16.6 1.0
CA A:CA204 3.9 14.8 1.0
O F:HOH302 4.1 22.7 1.0
CG F:GLU79 4.2 15.8 1.0
O A:HOH309 4.3 34.2 1.0
CG A:GLU79 4.3 15.9 1.0
O A:HOH346 4.4 53.8 1.0
NZ A:LYS23 4.4 22.3 0.5
O21 A:BCN205 4.4 17.5 1.0
OD1 J:ASN103 4.5 43.9 1.0
OE1 F:GLU79 4.5 16.5 1.0
O A:HOH306 4.5 31.8 1.0
O6 A:BCN203 4.6 23.3 1.0
CB J:ASN103 4.9 37.8 1.0
O J:ASN103 4.9 38.7 1.0
NZ F:LYS23 5.0 35.0 1.0

Calcium binding site 2 out of 10 in 5ele

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Calcium binding site 2 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:14.8
occ:1.00
 O6 A:BCN203 2.2 23.3 1.0
O F:HOH302 2.3 22.7 1.0
OE2 A:GLU79 2.3 16.3 1.0
O4 A:BCN203 2.4 24.5 1.0
O21 A:BCN203 2.4 18.6 1.0
OE1 F:GLU79 2.5 16.5 1.0
OE2 F:GLU79 2.5 17.5 1.0
CD F:GLU79 2.8 16.6 1.0
C3 A:BCN203 3.2 26.4 1.0
N1 A:BCN203 3.2 25.1 1.0
C4 A:BCN203 3.3 24.6 1.0
C6 A:BCN203 3.3 25.2 1.0
C2 A:BCN203 3.3 21.7 1.0
CD A:GLU79 3.4 17.5 1.0
C1 A:BCN203 3.6 23.4 1.0
C5 A:BCN203 3.6 24.7 1.0
CA A:CA201 3.9 14.5 1.0
O A:HOH302 4.0 25.6 1.0
CG A:GLU79 4.2 15.9 1.0
O6 A:BCN205 4.2 29.6 1.0
NZ F:LYS23 4.2 35.0 1.0
O A:HOH309 4.3 34.2 1.0
O F:HOH318 4.3 36.9 1.0
ND2 E:ASN103 4.3 40.3 1.0
OE1 A:GLU79 4.4 16.2 1.0
CG F:GLU79 4.4 15.8 1.0
O22 A:BCN203 4.5 18.0 1.0
CB E:ASN103 4.8 38.8 1.0

Calcium binding site 3 out of 10 in 5ele

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Calcium binding site 3 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:15.8
occ:1.00
 O6 B:BCN203 2.1 33.9 1.0
O22 B:BCN203 2.3 20.0 1.0
OE2 J:GLU79 2.4 18.5 1.0
O B:HOH303 2.4 27.1 1.0
OE1 B:GLU79 2.4 17.0 1.0
O4 B:BCN203 2.5 27.6 1.0
OE2 B:GLU79 2.5 17.7 1.0
CD B:GLU79 2.9 17.9 1.0
C6 B:BCN203 3.0 31.5 1.0
N1 B:BCN203 3.2 25.8 1.0
C2 B:BCN203 3.2 21.9 1.0
C4 B:BCN203 3.3 26.2 1.0
C3 B:BCN203 3.3 26.4 1.0
C1 B:BCN203 3.5 23.7 1.0
C5 B:BCN203 3.5 27.9 1.0
CD J:GLU79 3.5 16.6 1.0
CA B:CA204 3.9 13.9 1.0
O A:HOH334 4.2 25.9 1.0
CG J:GLU79 4.2 15.3 1.0
O B:HOH304 4.3 38.4 1.0
CG B:GLU79 4.4 14.9 1.0
O6 B:BCN201 4.4 24.0 1.0
O21 B:BCN203 4.4 21.5 1.0
NZ B:LYS23 4.4 26.6 0.5
ND2 I:ASN103 4.4 40.5 1.0
OE1 J:GLU79 4.5 18.1 1.0
O B:HOH354 4.5 35.3 1.0
O J:HOH302 4.6 31.6 1.0
CB I:ASN103 4.9 38.2 1.0

Calcium binding site 4 out of 10 in 5ele

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Calcium binding site 4 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:13.9
occ:1.00
 O6 B:BCN201 2.3 24.0 1.0
OE2 B:GLU79 2.3 17.7 1.0
O21 B:BCN201 2.4 19.3 1.0
O A:HOH334 2.4 25.9 1.0
OE1 J:GLU79 2.5 18.1 1.0
O4 B:BCN201 2.5 22.9 1.0
OE2 J:GLU79 2.5 18.5 1.0
CD J:GLU79 2.9 16.6 1.0
C6 B:BCN201 3.0 25.0 1.0
N1 B:BCN201 3.1 24.5 1.0
C2 B:BCN201 3.2 22.8 1.0
C3 B:BCN201 3.3 23.8 1.0
C4 B:BCN201 3.3 24.5 1.0
C5 B:BCN201 3.4 23.3 1.0
CD B:GLU79 3.5 17.9 1.0
C1 B:BCN201 3.5 24.9 1.0
CA B:CA202 3.9 15.8 1.0
O B:HOH303 4.0 27.1 1.0
CG B:GLU79 4.2 14.9 1.0
O J:HOH307 4.2 28.4 0.6
O B:HOH304 4.3 38.4 1.0
CG J:GLU79 4.4 15.3 1.0
O22 B:BCN201 4.4 21.9 1.0
OE1 B:GLU79 4.4 17.0 1.0
O B:HOH308 4.6 35.7 1.0
O6 B:BCN203 4.7 33.9 1.0
ND2 A:ASN103 4.7 44.8 1.0
O A:ASN103 4.9 42.6 1.0
CB A:ASN103 4.9 38.8 1.0

Calcium binding site 5 out of 10 in 5ele

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Calcium binding site 5 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:15.5
occ:1.00
 O4 C:BCN203 2.2 25.4 1.0
O C:HOH301 2.3 24.6 1.0
O6 C:BCN203 2.3 21.9 1.0
O22 C:BCN203 2.3 16.5 1.0
OE2 I:GLU79 2.3 17.8 1.0
OE1 C:GLU79 2.5 20.4 1.0
OE2 C:GLU79 2.6 21.6 1.0
N1 C:BCN203 2.8 23.1 1.0
CD C:GLU79 2.9 20.6 1.0
C4 C:BCN203 3.2 25.6 1.0
C2 C:BCN203 3.3 20.6 1.0
C6 C:BCN203 3.3 20.6 1.0
C5 C:BCN203 3.4 21.1 1.0
CD I:GLU79 3.5 18.8 1.0
C1 C:BCN203 3.5 20.7 1.0
C3 C:BCN203 3.6 23.5 1.0
NZ C:LYS23 3.7 26.8 0.5
CA C:CA204 4.0 15.2 1.0
O C:HOH361 4.0 27.4 1.0
CG I:GLU79 4.2 17.0 1.0
NZ I:LYS23 4.3 21.2 0.5
CG C:GLU79 4.4 18.8 1.0
O21 C:BCN203 4.4 18.4 1.0
O4 C:BCN201 4.4 22.7 1.0
OE1 I:GLU79 4.5 18.9 1.0
OD1 H:ASN103 4.6 39.7 1.0
O I:HOH302 4.6 17.2 0.5
O H:ASN103 4.9 38.7 1.0
CB H:ASN103 5.0 30.8 1.0

Calcium binding site 6 out of 10 in 5ele

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Calcium binding site 6 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:15.2
occ:1.00
 O4 C:BCN201 2.2 22.7 1.0
OE2 C:GLU79 2.3 21.6 1.0
O C:HOH361 2.4 27.4 1.0
O6 C:BCN201 2.4 21.5 1.0
O21 C:BCN201 2.4 18.9 1.0
OE1 I:GLU79 2.5 18.9 1.0
OE2 I:GLU79 2.6 17.8 1.0
N1 C:BCN201 2.7 21.8 1.0
CD I:GLU79 2.9 18.8 1.0
C4 C:BCN201 3.3 23.1 1.0
C2 C:BCN201 3.3 21.8 1.0
C6 C:BCN201 3.4 20.5 1.0
CD C:GLU79 3.5 20.6 1.0
C5 C:BCN201 3.5 21.1 1.0
C1 C:BCN201 3.5 22.6 1.0
C3 C:BCN201 3.5 21.7 1.0
CA C:CA202 4.0 15.5 1.0
O C:HOH301 4.0 24.6 1.0
CG C:GLU79 4.1 18.8 1.0
O I:HOH360 4.3 37.4 1.0
CG I:GLU79 4.4 17.0 1.0
O C:HOH302 4.4 35.1 1.0
OE1 C:GLU79 4.5 20.4 1.0
ND2 B:ASN103 4.5 36.1 1.0
O22 C:BCN201 4.5 20.2 1.0
O4 C:BCN203 4.6 25.4 1.0
NZ I:LYS23 4.7 21.2 0.5
CB B:ASN103 5.0 36.5 1.0

Calcium binding site 7 out of 10 in 5ele

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Calcium binding site 7 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:14.2
occ:1.00
 O4 D:BCN203 2.3 24.2 1.0
OE2 H:GLU79 2.3 16.9 1.0
O6 D:BCN203 2.4 19.7 1.0
O22 D:BCN203 2.4 18.1 1.0
O G:HOH333 2.4 28.0 1.0
OE1 D:GLU79 2.5 17.6 1.0
OE2 D:GLU79 2.5 17.3 1.0
N1 D:BCN203 2.8 22.0 1.0
CD D:GLU79 2.8 16.4 1.0
C2 D:BCN203 3.3 19.6 1.0
C4 D:BCN203 3.3 24.2 1.0
C6 D:BCN203 3.4 21.2 1.0
C5 D:BCN203 3.5 22.2 1.0
CD H:GLU79 3.5 16.2 1.0
C3 D:BCN203 3.5 22.2 1.0
C1 D:BCN203 3.5 21.0 1.0
CA D:CA204 4.0 14.6 1.0
O D:HOH352 4.2 23.6 1.0
O D:HOH303 4.2 39.9 1.0
CG H:GLU79 4.2 15.2 1.0
O D:HOH309 4.2 37.4 1.0
CG D:GLU79 4.3 14.9 1.0
O H:HOH303 4.4 33.1 1.0
O21 D:BCN203 4.5 17.7 1.0
OE1 H:GLU79 4.5 17.6 1.0
O6 D:BCN201 4.5 26.9 1.0
OXT G:ASN103 4.8 55.7 1.0
OD1 G:ASN103 4.9 47.7 1.0
CB G:ASN103 5.0 46.7 1.0

Calcium binding site 8 out of 10 in 5ele

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Calcium binding site 8 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:14.6
occ:1.00
 O6 D:BCN201 2.2 26.9 1.0
O21 D:BCN201 2.3 15.8 1.0
OE2 D:GLU79 2.3 17.3 1.0
OE1 H:GLU79 2.4 17.6 1.0
O4 D:BCN201 2.4 26.6 1.0
O D:HOH352 2.5 23.6 1.0
OE2 H:GLU79 2.5 16.9 1.0
CD H:GLU79 2.8 16.2 1.0
N1 D:BCN201 3.1 24.5 1.0
C6 D:BCN201 3.2 28.5 1.0
C2 D:BCN201 3.2 21.3 1.0
C3 D:BCN201 3.2 25.4 1.0
C4 D:BCN201 3.3 25.8 1.0
C1 D:BCN201 3.5 22.9 1.0
C5 D:BCN201 3.5 25.6 1.0
CD D:GLU79 3.5 16.4 1.0
CA D:CA202 4.0 14.2 1.0
O G:HOH333 4.1 28.0 1.0
O H:HOH321 4.1 40.3 1.0
CG D:GLU79 4.2 14.9 1.0
O D:HOH303 4.2 39.9 1.0
ND2 C:ASN103 4.3 49.3 1.0
CG H:GLU79 4.3 15.2 1.0
O22 D:BCN201 4.4 18.4 1.0
O D:HOH311 4.5 32.9 1.0
OE1 D:GLU79 4.6 17.6 1.0
O4 D:BCN203 4.6 24.2 1.0
CB C:ASN103 4.7 43.1 1.0
O D:HOH380 4.9 51.1 1.0

Calcium binding site 9 out of 10 in 5ele

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Calcium binding site 9 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:13.4
occ:1.00
 O4 E:BCN203 2.2 29.2 1.0
OE2 G:GLU79 2.3 16.5 1.0
O21 E:BCN203 2.4 17.7 1.0
O6 E:BCN203 2.4 22.2 1.0
OE1 E:GLU79 2.4 16.6 1.0
O F:HOH332 2.4 27.9 1.0
OE2 E:GLU79 2.5 15.8 1.0
N1 E:BCN203 2.7 22.9 1.0
CD E:GLU79 2.8 16.7 1.0
C4 E:BCN203 3.2 29.0 1.0
C2 E:BCN203 3.3 19.9 1.0
C6 E:BCN203 3.4 21.8 1.0
C5 E:BCN203 3.4 22.9 1.0
C3 E:BCN203 3.5 24.6 1.0
CD G:GLU79 3.5 16.5 1.0
C1 E:BCN203 3.6 21.8 1.0
CA E:CA204 3.9 14.5 1.0
O E:HOH363 4.0 27.6 1.0
CG G:GLU79 4.2 14.3 1.0
O6 E:BCN201 4.3 27.3 1.0
CG E:GLU79 4.3 15.3 1.0
OE1 G:GLU79 4.4 18.8 1.0
O22 E:BCN203 4.5 17.1 1.0
O E:HOH303 4.5 29.9 1.0
OD1 F:ASN103 4.6 42.0 1.0
OXT F:ASN103 4.8 36.0 1.0

Calcium binding site 10 out of 10 in 5ele

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Calcium binding site 10 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca204

b:14.5
occ:1.00
 O6 E:BCN201 1.9 27.3 1.0
OE2 E:GLU79 2.3 15.8 1.0
O22 E:BCN201 2.3 19.4 1.0
O E:HOH363 2.4 27.6 1.0
O4 E:BCN201 2.4 20.8 1.0
OE1 G:GLU79 2.5 18.8 1.0
OE2 G:GLU79 2.6 16.5 1.0
CD G:GLU79 2.9 16.5 1.0
C6 E:BCN201 3.1 27.9 1.0
N1 E:BCN201 3.1 23.8 1.0
C2 E:BCN201 3.3 20.8 1.0
C5 E:BCN201 3.4 24.9 1.0
C4 E:BCN201 3.4 23.1 1.0
C3 E:BCN201 3.5 23.9 1.0
CD E:GLU79 3.5 16.7 1.0
C1 E:BCN201 3.5 23.9 1.0
CA E:CA202 3.9 13.4 1.0
O F:HOH332 4.0 27.9 1.0
O G:HOH373 4.2 36.3 1.0
CG E:GLU79 4.2 15.3 1.0
O4 E:BCN203 4.3 29.2 1.0
CG G:GLU79 4.4 14.3 1.0
OE1 E:GLU79 4.4 16.6 1.0
O21 E:BCN201 4.5 20.0 1.0
O D:HOH344 4.5 36.3 1.0
ND2 D:ASN103 4.7 47.8 1.0

Reference:

J.E.Heggelund, D.Burschowsky, V.A.Bjrnestad, V.Hodnik, G.Anderluh, U.Krengel. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Plos Pathog. V. 12 05567 2016.
ISSN: ESSN 1553-7374
PubMed: 27082955
DOI: 10.1371/JOURNAL.PPAT.1005567
Page generated: Sun Jul 14 18:40:11 2024

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